PaperBLAST

PaperBLAST Hits for b1760 (90 a.a., MSRALFAVVL...)

Show query sequence

>b1760
MSRALFAVVLAFPLIALANPHYRPDVEVNVPPEVFSSGGQSAQPCTQCCVYQDQNYSEGA
VIKAEGILLQCQRDDKTLSTNPLVWRRVKP

Running BLASTp...

Found 3 similar proteins in the literature:

YnjH / b1760 DUF1496 domain-containing protein YnjH from Escherichia coli K-12 substr. MG1655 (see paper)
b1760 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
100% identity, 100% coverage

• Identification of a target gene and activating stimulus for the YpdA/YpdB histidine kinase/response regulator system in Escherichia coli
  Fried, Journal of bacteriology 2013
  • “...0.01 0.01 103 entE ynjH ygbL yahM iraP ygbK yehS b0594 b1760 b2738 b0327 b0382 b2737 b2124 110 740 130 210 330 220 1,680 60 1,860 340 580 1,030 690 16,130 0.9...”
• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013
• Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli
  Zhao, Nucleic acids research 2007
  • “...yjdA Conserved hypothetical protein Not classified 12.3 5.3 b3525 yhjH Conserved protein Unknown 9.6 1.9 b1760 ynjH Conserved hypothetical protein Unknown 6.9 7.9 b1742 ydjR Conserved hypothetical protein Unknown 4.7 4.5 b0250 ykfB CP4-6 prophage Unknown 3.7 4.0 b0764 modB Molybdate transport protein Transport of small...”
• In silico prediction and functional validation of sigma28-regulated genes in Chlamydia and Escherichia coli
  Yu, Journal of bacteriology 2006
  • “...tested for in vitro activity Gene name b0132 b0763 b1760 yadD modA ynjH b1915 b3204 b3490 b4083 yecF ptsN yhiL yjcS Function Hypothetical protein Molybdate ABC...”
• Differential gene expression for investigation of Escherichia coli biofilm inhibition by plant extract ursolic acid
  Ren, Applied and environmental microbiology 2005
  • “...and/or 30 g of ursolic acid/ml (Table 3), such as b1566, b1760, b2674, yjjS, yrfH, and yrfI. b1566 is also known as flxA, and its expression is dependent on the...”
  • “...functions cirA entE fxsA mlc osmE prlC b1194 b1321 b1566 b1760 yadN b2674 ybeD ycjF yeiE yhdM yhjH yjjS yrfG b2155 b0594 b4140 b1594 b1739 b3498 b1194 b1321...”
• Identification and mapping of self-assembling protein domains encoded by the Escherichia coli K-12 genome by use of lambda repressor fusions
  Mariño-Ramírez, Journal of bacteriology 2004
  • “...b4192 b4249 b4295 b0515 b1145 b1330 b1524 b1595 b1760 b2434 b2549 b2875 b3071 b3193 b3199 b3830 b4212 b4218 COG0393 COG1335 COG2323 COG1335 COG3132 COG1607...”

SL1344_1235 YnjH family protein from Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
STM1300 putative periplasmic protein from Salmonella typhimurium LT2
73% identity, 98% coverage

• Fatty Acid Homeostasis Tunes Flagellar Motility by Activating Phase 2 Flagellin Expression, Contributing to Salmonella Gut Colonization
  Hoshino, Infection and immunity 2022 (secret)
• Structure-based analyses of Salmonella RcsB variants unravel new features of the Rcs regulon
  Huesa, Nucleic acids research 2021
  • “...2 fold change (WT) log 2 fold change (M88A) log 2 fold change (L108A) 1337038 SL1344_1235 gene promoter-5UTR + 32 1337044 6 to 8 TGAGAATATACTTA 3.35 1.43 2.97 844864 SL1344_0758 modA gene 5UTR + 64 844835 29 to 43 TGGGAAACCCCTGA 2.22 1.67 1979777 SL1344_1860 flhD gene...”
• Regulatory Cross Talk between Motility and Interbacterial Communication in Salmonella enterica Serovar Typhimurium
  Plitnick, Journal of bacteriology 2021 (secret)
• Genome-scale co-expression network comparison across Escherichia coli and Salmonella enterica serovar Typhimurium reveals significant conservation at the regulon level of local regulators despite their dissimilar lifestyles
  Zarrineh, PloS one 2014
  • “...From 20 genes detected as variable part in S. enterica just four genes (srfB, srfC, STM1300, STM2314) has not previously been identified as motility and flagerlla synthesis in E. coli . The other 16 genes could be detected in E. coli if the lower threshold would...”
• Uncovering a large set of genes that affect surface motility in Salmonella enterica serovar Typhimurium
  Wang, Journal of bacteriology 2006
  • “...genes flgB cheY Putative class 3 cheV mcpB mcpC STM1300 ycgR yghW yhjH Putative motility genes with profiles different from known or similar to known motility...”

YPTB2092 putative exported protein from Yersinia pseudotuberculosis IP 32953
YPO2166 putative exported protein from Yersinia pestis CO92
46% identity, 91% coverage

• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...YPTB1996 YPO2004 putative membrane protein 2.041 (0.002) YPTB2000 YPO2012 putative membrane protein 0.256 (< 0.001) YPTB2092 YPO2166 putative exported protein 0.671 (0.027) YPTB2114 YPO2191 hypothetical protein 0.28 (< 0.001) YPTB2148 YPO2226 hypothetical protein 1.855 (0.007) YPTB2151 (osmB) YPO2229 osmotically inducible lipoprotein B precursoR 2.229 (< 0.001)...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...YPO2004 putative membrane protein 2.041 (0.002) YPTB2000 YPO2012 putative membrane protein 0.256 (< 0.001) YPTB2092 YPO2166 putative exported protein 0.671 (0.027) YPTB2114 YPO2191 hypothetical protein 0.28 (< 0.001) YPTB2148 YPO2226 hypothetical protein 1.855 (0.007) YPTB2151 (osmB) YPO2229 osmotically inducible lipoprotein B precursoR 2.229 (< 0.001) 1.413...”

New Search

Statistics

How It Works

PaperBLAST builds a database of protein sequences that are linked to scientific articles. These links come from automated text searches against the articles in EuropePMC and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot, BRENDA, CAZy (as made available by dbCAN), BioLiP, CharProtDB, MetaCyc, EcoCyc, TCDB, REBASE, the Fitness Browser, and a subset of the European Nucleotide Archive with the /experiment tag. Given this database and a protein sequence query, PaperBLAST uses protein-protein BLAST to find similar sequences with E < 0.001.

To build the database, we query EuropePMC with locus tags, with RefSeq protein identifiers, and with UniProt accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use queries of the form "locus_tag AND genus_name" to try to ensure that the paper is actually discussing that gene. Because EuropePMC indexes most recent biomedical papers, even if they are not open access, some of the links may be to papers that you cannot read or that our computers cannot read. We query each of these identifiers that appears in the open access part of EuropePMC, as well as every locus tag that appears in the 500 most-referenced genomes, so that a gene may appear in the PaperBLAST results even though none of the papers that mention it are open access. We also incorporate text-mined links from EuropePMC that link open access articles to UniProt or RefSeq identifiers. (This yields some additional links because EuropePMC uses different heuristics for their text mining than we do.)

For every article that mentions a locus tag, a RefSeq protein identifier, or a UniProt accession, we try to select one or two snippets of text that refer to the protein. If we cannot get access to the full text, we try to select a snippet from the abstract, but unfortunately, unique identifiers such as locus tags are rarely provided in abstracts.

PaperBLAST also incorporates manually-curated protein functions:

• Proteins from NCBI's RefSeq are included if a GeneRIF entry links the gene to an article in PubMed^®. GeneRIF also provides a short summary of the article's claim about the protein, which is shown instead of a snippet.
• Proteins from Swiss-Prot (the curated part of UniProt) are included if the curators identified experimental evidence for the protein's function (evidence code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that describe the protein's function are shown (with bold headings).
• Proteins from BRENDA, a curated database of enzymes, are included if they are linked to a paper in PubMed and their full sequence is known.
• Every protein from the non-redundant subset of BioLiP, a database of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself does not include descriptions of the proteins, those are taken from the Protein Data Bank. Descriptions from PDB rely on the original submitter of the structure and cannot be updated by others, so they may be less reliable. (For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every ligand is represented among a group of structures with similar sequences, but for PaperBLAST, we use the non-redundant set provided by BioLiP.)
• Every protein from EcoCyc, a curated database of the proteins in Escherichia coli K-12, is included, regardless of whether they are characterized or not.
• Proteins from the MetaCyc metabolic pathway database are included if they are linked to a paper in PubMed and their full sequence is known.
• Proteins from the Transport Classification Database (TCDB) are included if they have known substrate(s), have reference(s), and are not described as uncharacterized or putative. (Some of the references are not visible on the PaperBLAST web site.)
• Every protein from CharProtDB, a database of experimentally characterized protein annotations, is included.
• Proteins from the CAZy database of carbohydrate-active enzymes are included if they are associated with an Enzyme Classification number. Even though CAZy does not provide links from individual protein sequences to papers, these should all be experimentally-characterized proteins.
• Proteins from the REBASE database of restriction enzymes are included if they have known specificity.
• Every protein with an evidence-based reannotation (based on mutant phenotypes) in the Fitness Browser is included.
• Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators) with experimentally-determined DNA binding sites from the PRODORIC database of gene regulation in prokaryotes.
• Putative transcription factors from RegPrecise that have manually-curated predictions for their binding sites. These predictions are based on conserved putative regulatory sites across genomes that contain similar transcription factors, so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
• Coding sequence (CDS) features from the European Nucleotide Archive (ENA) are included if the /experiment tag is set (implying that there is experimental evidence for the annotation), the nucleotide entry links to paper(s) in PubMed, and the nucleotide entry is from the STD data class (implying that these are targeted annotated sequences, not from shotgun sequencing). Also, to filter out genes whose transcription or translation was detected, but whose function was not studied, nucleotide entries or papers with more than 25 such proteins are excluded. Descriptions from ENA rely on the original submitter of the sequence and cannot be updated by others, so they may be less reliable.

Except for GeneRIF and ENA, the curated entries include a short curated description of the protein's function. For entries from BioLiP, the protein's function may not be known beyond binding to the ligand. Many of these entries also link to articles in PubMed.

For more information see the PaperBLAST paper (mSystems 2017) or the code. You can download PaperBLAST's database here.

Changes to PaperBLAST since the paper was written:

• November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
• February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
• June 2022: incorporated some coding sequences from ENA with the /experiment tag.
• March 2022: incorporated BioLiP.
• April 2020: incorporated TCDB.
• April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
• February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
• January 2018: incorporated BRENDA.
• December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
• September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.

Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.

Secrets

PaperBLAST cannot provide snippets for many of the papers that are published in non-open-access journals. This limitation applies even if the paper is marked as "free" on the publisher's web site and is available in PubmedCentral or EuropePMC. If a journal that you publish in is marked as "secret," please consider publishing elsewhere.

Omissions from the PaperBLAST Database

Many important articles are missing from PaperBLAST, either because the article's full text is not in EuropePMC (as for many older articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an article that characterizes a protein's function but is missing from PaperBLAST, please notify the curators at UniProt or add an entry to GeneRIF. Entries in either of these databases will eventually be incorporated into PaperBLAST. Note that to add an entry to UniProt, you will need to find the UniProt identifier for the protein. If the protein is not already in UniProt, you can ask them to create an entry. To add an entry to GeneRIF, you will need an NCBI Gene identifier, but unfortunately many prokaryotic proteins in RefSeq do not have corresponding Gene identifers.

References

PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.

Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.

Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.

UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.

BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.

The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.

CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.

The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.

The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.

REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.

Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.